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Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species

https://doi.org/10.1101/gr.1416703
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Spontaneous microdeletions and microinsertions in a transgenic mouse mutation detection system: analysis of age, tissue, and sequence specificity
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The Use of Imperfect Microsatellites for DNA Fingerprinting and Population Genetics
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Notes on the definition and nomenclature of tandemly repetitive DNA sequences
inferredcites →https://doi.org/10.1007/bf00167107openalex-snapshot
Simple repetitive DNA sequences from primates: Compilation and analysis
inferredcites →https://doi.org/10.1007/pl00006161openalex-snapshot
The Length Distribution of Perfect Dimer Repetitive DNA Is Consistent with Its Evolution by an Unbiased Single-Step Mutation Process
inferredcites →https://doi.org/10.1007/pl00006474openalex-snapshot
Evolution of Microsatellites in the Yeast Saccharomyces cerevisiae: Role of Length and Number of Repeated Units
inferredcites →https://doi.org/10.1007/s00239-002-2366-5openalex-snapshot
A DNA Sequence Evolution Analysis Generalized by Simulation and the Markov Chain Monte Carlo Method Implicates Strand Slippage in a Majority of Insertions and Deletions
inferredcites →https://doi.org/10.1007/s004120000089openalex-snapshot
Evolutionary dynamics of microsatellite DNA
inferredcites →https://doi.org/10.1016/s0168-9525(00)02139-9openalex-snapshot
Microsatellite mutations in the germline:
inferredcites →https://doi.org/10.1016/s0960-9822(98)70989-3openalex-snapshot
Genome evolution: Are microsatellites really simple sequences?
inferredcites →https://doi.org/10.1016/s1097-2765(02)00575-0openalex-snapshot
Mismatch Repair-Driven Mutational Bias in D. melanogaster
inferredcites →https://doi.org/10.1017/s001667230000478xopenalex-snapshot
Insertions, substitutions, and the origin of microsatellites
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/74238openalex-snapshot
The direction of microsatellite mutations is dependent upon allele length
inferredcites →https://doi.org/10.1038/74249openalex-snapshot
Heterogeneous mutation processes in human microsatellite DNA sequences
inferredcites →https://doi.org/10.1038/ng822openalex-snapshot
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes
inferredcites →https://doi.org/10.1073/pnas.122067599openalex-snapshot
Microsatellite evolution inferred from human– chimpanzee genomic sequence alignments
inferredcites →https://doi.org/10.1073/pnas.202336899openalex-snapshot
Hitchhiking mapping: A population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster
inferredcites →https://doi.org/10.1073/pnas.93.13.6470openalex-snapshot
Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications.
inferredcites →https://doi.org/10.1073/pnas.94.10.5237openalex-snapshot
Characteristic enrichment of DNA repeats in different genomes
inferredcites →https://doi.org/10.1073/pnas.94.3.1041openalex-snapshot
Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci
inferredcites →https://doi.org/10.1073/pnas.95.18.10774openalex-snapshot
Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations
inferredcites →https://doi.org/10.1073/pnas.95.4.1647openalex-snapshot
Abundant microsatellite polymorphism in Saccharomyces cerevisiae , and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae , result from strong mutation pressures and a variety of selective forces
inferredcites →https://doi.org/10.1073/pnas.95.9.5172openalex-snapshot
Homology-directed repair is a major double-strand break repair pathway in mammalian cells
inferredcites →https://doi.org/10.1086/301869openalex-snapshot
Mutation Rate in Human Microsatellites: Influence of the Structure and Length of the Tandem Repeat
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Constraints on Allele Size at Microsatellite Loci: Implications for Genetic Differentiation
inferredcites →https://doi.org/10.1093/genetics/155.3.1213openalex-snapshot
Long Microsatellite Alleles inDrosophila melanogasterHave a Downward Mutation Bias and Short Persistence Times, Which Cause Their Genome-Wide Underrepresentation
inferredcites →https://doi.org/10.1093/genetics/159.2.839openalex-snapshot
Dynamics of Microsatellite Divergence Under Stepwise Mutation and Proportional Slippage/Point Mutation Models
inferredcites →https://doi.org/10.1093/nar/20.2.211openalex-snapshot
Slippage synthesis of simple sequence DNA
inferredcites →https://doi.org/10.1093/nar/23.19.3882openalex-snapshot
Microsatellite variation in North American populations ofDrosophila melanogaster
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Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci
inferredcites →https://doi.org/10.1093/nar/gkg178openalex-snapshot
Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites
inferredcites →https://doi.org/10.1093/oso/9780198504085.001.0001openalex-snapshot
Microsatellites: Evolution and Applications
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003903openalex-snapshot
Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025964openalex-snapshot
A threshold size for microsatellite expansion
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026411openalex-snapshot
Microsatellite Variability Differs Between Dinucleotide Repeat Motifs—Evidence from Drosophila melanogaster
inferredcites →https://doi.org/10.1101/gr.10.7.967openalex-snapshot
Microsatellites in Different Eukaryotic Genomes: Survey and Analysis
inferredcites →https://doi.org/10.1101/gr.138802openalex-snapshot
Tandem Repeats in Protein Coding Regions of Primate Genes
inferredcites →https://doi.org/10.1101/gr.163101openalex-snapshot
Genome-Scale Compositional Comparisons in Eukaryotes
inferredcites →https://doi.org/10.1126/science.291.5509.1738openalex-snapshot
Genealogical and Evolutionary Inference with the Human Y Chromosome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Transposable Element Orientation Bias in the Drosophila melanogaster Genome
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Local Mutagenic Impact of Insertions of LTR Retrotransposons on the Mouse Genome
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Mutation Biases and Mutation Rate Variation Around Very Short Human Microsatellites Revealed by Human–Chimpanzee–Orangutan Genomic Sequence Alignments
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Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes
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Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana
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Short tandem repeats delineate gene bodies across eukaryotes
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Inherent instability of simple DNA repeats shapes an evolutionarily stable distribution of repeat lengths
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Selection on MHC-linked microsatellite loci in sheep populations
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Usefulness of microsatellite loci for differentiating between Dibothriocephalus dendriticus and Dibothriocephalus ditremus (Cestoda: Diphyllobothriidea)
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DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach
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Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome
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Elevated Basal Slippage Mutation Rates among the Canidae
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Long Perfect Dinucleotide Repeats Are Typical of Vertebrates, Show Motif Preferences and Size Convergence
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The Relationship Between Microsatellite Polymorphism and Recombination Hot Spots in the Human Genome
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Hypermutability of Genes in Homo sapiens Due to the Hosting of Long Mono-SSR
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Genome Nucleotide Composition Shapes Variation in Simple Sequence Repeats
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InSatDb: a microsatellite database of fully sequenced insect genomes
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Megasatellite formation and evolution in vertebrates
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Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea
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Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
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Genome-wide evidence for selection acting on single amino acid repeats
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Silene tatarica microsatellites are frequently located in repetitive DNA
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Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates
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Repetitive DNA elements as mediators of genomic change in response to environmental cues
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RECONSTRUCTING ORIGINS OF LOSS OF SELF-INCOMPATIBILITY AND SELFING IN NORTH AMERICAN ARABIDOPSIS LYRATA: A POPULATION GENETIC CONTEXT
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Current trends in microsatellite genotyping
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Genome‐wide characterization of microsatellites in cobia Rachycentron canadum (Linnaeus, 1766): Survey and analysis of their abundance and diversity
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Genome Plasticity of Aspergillus Species
inferred← citeshttps://doi.org/10.1128/mbio.01055-13openalex-snapshot
Intracytoplasmic Copper Homeostasis Controls Cytochrome c Oxidase Production
inferred← citeshttps://doi.org/10.1134/s0026893319010084openalex-snapshot
Imperfect and Compound Microsatellites in the Genomes of Burkholderia pseudomallei Strains
inferred← citeshttps://doi.org/10.1134/s0026898419010087openalex-snapshot
Идентификация и характеристика вырожденных и сложных микросателлитов в геномах штаммов Burkholderia pseudomallei
inferred← citeshttps://doi.org/10.1134/s1022795418030031openalex-snapshot
Characteristics of the Genetic Structure of Snow Sheep (Ovis nivicola lydekkeri) of the Verkhoyansk Mountain Chain
inferred← citeshttps://doi.org/10.1134/s2079059718010057openalex-snapshot
Study of Allele Pool and Genetic Structure of Russian Population of Lowland-Caucasian Line of European Bison (Bison bonasus)
inferred← citeshttps://doi.org/10.1139/g05-004openalex-snapshot
Evolution of a triplet repeat in a conifer
inferred← citeshttps://doi.org/10.1158/2159-8290.cd-20-0790openalex-snapshot
DNA Polymerase and Mismatch Repair Exert Distinct Microsatellite Instability Signatures in Normal and Malignant Human Cells
inferred← citeshttps://doi.org/10.1159/000527049openalex-snapshot
Transcriptional Analysis of Microsatellites in Velvetbean Caterpillar Anticarsia gemmatalis Hübner, 1818
inferred← citeshttps://doi.org/10.1186/1471-2105-8-125openalex-snapshot
Detecting microsatellites within genomes: significant variation among algorithms
inferred← citeshttps://doi.org/10.1186/1471-2164-11-277openalex-snapshot
Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach
inferred← citeshttps://doi.org/10.1186/1471-2164-11-428openalex-snapshot
Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness
inferred← citeshttps://doi.org/10.1186/1471-2164-14-103openalex-snapshot
Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome
inferred← citeshttps://doi.org/10.1186/1471-2164-7-245openalex-snapshot
Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus
inferred← citeshttps://doi.org/10.1186/1471-2164-7-269openalex-snapshot
Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
inferred← citeshttps://doi.org/10.1186/1471-2164-8-174openalex-snapshot
Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus
inferred← citeshttps://doi.org/10.1186/1471-2164-8-225openalex-snapshot
EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes
inferred← citeshttps://doi.org/10.1186/1471-2164-9-612openalex-snapshot
Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites
inferred← citeshttps://doi.org/10.1186/1756-0500-6-249openalex-snapshot
Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species
inferred← citeshttps://doi.org/10.1186/gb-2009-10-6-r59openalex-snapshot
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins
inferred← citeshttps://doi.org/10.1186/s12863-023-01108-7openalex-snapshot
Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera)
inferred← citeshttps://doi.org/10.1186/s12864-021-07752-6openalex-snapshot
Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions
inferred← citeshttps://doi.org/10.1186/s40555-014-0063-xopenalex-snapshot
Genetic variation of the striped hamster (Cricetulus barabensis) and the impact of population density and environmental factors
inferred← citeshttps://doi.org/10.1360/982005-270openalex-snapshot
Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002573openalex-snapshot
A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1371/journal.pone.0026933openalex-snapshot
Fast and Cost-Effective Mining of Microsatellite Markers Using NGS Technology: An Example of a Korean Water Deer Hydropotes inermis argyropus
inferred← citeshttps://doi.org/10.1371/journal.pone.0040861openalex-snapshot
Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species
inferred← citeshttps://doi.org/10.1371/journal.pone.0101177openalex-snapshot
Microsatellite Repeat Instability Fuels Evolution of Embryonic Enhancers in Hawaiian Drosophila
inferred← citeshttps://doi.org/10.1371/journal.pone.0107043openalex-snapshot
Genotype Profile of Leishmania major Strains Isolated from Tunisian Rodent Reservoir Hosts Revealed by Multilocus Microsatellite Typing
inferred← citeshttps://doi.org/10.1371/journal.pone.0133667openalex-snapshot
Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species
inferred← citeshttps://doi.org/10.1371/journal.pone.0265548openalex-snapshot
High migratory propensity constitutes a single stock of an exploited cutlassfish species in the Northwest Pacific: A microsatellite approach
inferred← citeshttps://doi.org/10.1534/genetics.106.063677openalex-snapshot
Identification of Selective Sweeps Using a Dynamically Adjusted Number of Linked Microsatellites
inferred← citeshttps://doi.org/10.1534/genetics.107.076067openalex-snapshot
An Unusually Low Microsatellite Mutation Rate in Dictyostelium discoideum, an Organism With Unusually Abundant Microsatellites
inferred← citeshttps://doi.org/10.1534/genetics.111.132308openalex-snapshot
Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites
inferred← citeshttps://doi.org/10.15740/has/au/11.2/163-172openalex-snapshot
Tools for simple sequence repeat (SSR) markers
inferred← citeshttps://doi.org/10.17795/gct-26204openalex-snapshot
Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family
inferred← citeshttps://doi.org/10.17795/gct-26404openalex-snapshot
Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family
inferred← citeshttps://doi.org/10.17816/ecogen1524-10openalex-snapshot
Study of allele pool and genetic structure of russian population of lowland-caucasian line of European bison (Bison bonasus)
inferred← citeshttps://doi.org/10.18632/oncotarget.2933openalex-snapshot
Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2210303/v1openalex-snapshot
Microsatellite polymorphism based genetic variation among the natural populations of two sympatric species of Drosophila: D. bipectinate and D. malerkotliana
inferred← citeshttps://doi.org/10.26021/8100openalex-snapshot
Conservation and Evolution of Microsatellites in Vertebrate Genomes
inferred← citeshttps://doi.org/10.26686/wgtn.17134568openalex-snapshot
Genome-wide SNP analysis reveals patterns of population differentiation and adaptation of red rock lobster Jasus edwardsii
inferred← citeshttps://doi.org/10.26686/wgtn.17134568.v1openalex-snapshot
Genome-wide SNP analysis reveals patterns of population differentiation and adaptation of red rock lobster Jasus edwardsii
inferred← citeshttps://doi.org/10.3389/fgene.2019.00207openalex-snapshot
Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family
inferred← citeshttps://doi.org/10.3390/app12073219openalex-snapshot
Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy
inferred← citeshttps://doi.org/10.3390/genes11101114openalex-snapshot
A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization
inferred← citeshttps://doi.org/10.3390/ijms241411437openalex-snapshot
Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects?
inferred← citeshttps://doi.org/10.3390/v7042126openalex-snapshot
Genome Variability and Gene Content in Chordopoxviruses: Dependence on Microsatellites
inferred← citeshttps://doi.org/10.37247/paasc.1.22.18openalex-snapshot
Brown trout (Salmo trutta) Phylogentics
inferred← citeshttps://doi.org/10.3906/biy-1503-11openalex-snapshot
In silico genome-wide identification and analysis of microsatelliterepeats in the largest RNA virus family (Closteroviridae)
inferred← citeshttps://doi.org/10.4137/bbi.s561openalex-snapshot
Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis
inferred← citeshttps://doi.org/10.4137/ebo.s420openalex-snapshot
Detecting Microsatellites in Genome Data: Variance in Definitions and Bioinformatic Approaches Cause Systematic Bias
inferred← citeshttps://doi.org/10.4137/ebo.s6662openalex-snapshot
A Monte Carlo Method for Assessing the Quality of Duplication-Aware Alignment Algorithms
inferred← citeshttps://doi.org/10.4137/ebo.s9131openalex-snapshot
A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment
inferred← citeshttps://doi.org/10.4172/2153-0602.1000187openalex-snapshot
Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus
inferred← citeshttps://doi.org/10.47749/t/unicamp.2012.852523openalex-snapshot
Estudos taxonômicos e biossistemáticos no complexo Kielmeyera coriacea Mart.& Zucc. (Caloplyllaceae)
inferred← citeshttps://doi.org/10.53846/goediss-1744openalex-snapshot
Isolation, molecular characterisation and chromosomal location of repetitive DNA sequences in Brassica
inferred← citeshttps://doi.org/10.5772/34408openalex-snapshot
Analysis of Genetic Diversity and SSR Allelic Variation in Rubber Tree (Hevea brasilensis)
inferred← citeshttps://doi.org/10.5812/gct.14543openalex-snapshot
Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes
inferred← citeshttps://doi.org/10.5897/ajb2014.14116openalex-snapshot
Development of microsatellite markers for use in breeding catfish, Rhamdia sp.
inferred← citeshttps://doi.org/10.6026/97320630005402openalex-snapshot
Analysis of simple sequence repeats (SSRs) dynamics in fungus Fusarium graminearum
inferred← citeshttps://doi.org/10.6084/m9.figshare.14633714openalex-snapshot
Additional file 1 of Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
inferred← citeshttps://doi.org/10.6084/m9.figshare.14633717openalex-snapshot
Additional file 2 of Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
inferred← citeshttps://doi.org/10.6084/m9.figshare.14633720openalex-snapshot
Additional file 3 of Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
inferred← citeshttps://doi.org/10.6084/m9.figshare.14633723openalex-snapshot
Additional file 4 of Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
inferred← citeshttps://doi.org/10.6084/m9.figshare.14746489openalex-snapshot
Additional file 1 of Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions
inferred← citeshttps://doi.org/10.6084/m9.figshare.14746492openalex-snapshot
Additional file 2 of Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions
inferred← citeshttps://doi.org/10.6092/unibo/amsdottorato/660openalex-snapshot
Molecular markers for the assessment of genetic variability in threatened plant species
inferred← citeshttps://doi.org/10.70675/33889fbfz2424z41d8z86f4z7fa1c721ab39openalex-snapshot
Phylogeny and population genetics of the fish performing the largest migration known in freshwater, the Amazonian catfish "Brachyplatystoma rousseauxii" : revelations from the upper Madera Basin
inferred← citeshttps://doi.org/10.70675/3d7a8d9bz2c98z48dbzab21z3435d40f82deopenalex-snapshot
Prédiction de la qualité des bois de chêne pour l’élevage des vins et des alcools : comparaison des approches physicochimiques, sensorielles et moléculaires
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